Lineage analysis of oligodendrocytes from joint hindbrain (clusters 14, 4, 8, and 21)
Alexis Blanchet-Cohen
03 June, 2019
1 Setup
source("functions.R")
source("functions_sam.R")
library(cytokit)
library(kableExtra)
library(ggedit)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)sample <- c("joint_pons.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)1.1 Load Seurat objects
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_pons.seurat.Rda"))
seurat <- joint_pons1.2 Convert Seurat object to Monocle object.
No oligodendrocytes were found in the hindbrain at E12 and E15.
# Convert cluster numbers to format used in levels(seurat@ident)
selected_clusters <- c(14, 4, 8, 21)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)
# Colour vector is not available in this object for these cluster IDs, so they must be recovered a saved object. seurat@misc$colours and seurat@misc$colours_orig are identical vectors. Bug will be fixed later, according to Selin.
# First, recover corresponding new cluster ID.
load("/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02/palettes_joint.Rda")
seurat@misc$colours <- pal_jp
# Cluster columns also need to be renamed.
seurat@meta.data$cluster <- as.character(seurat@meta.data$cluster_joint)
monocle <- seurat_to_monocle(seurat, selected_clusters)
#monocle <- orderCells(monocle, reverse=TRUE)
colours <- monocle@experimentData@other$colours2 Monocle plots
2.1 Cell trajectories
p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)
plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)
plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)
p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
2.2 Differentially expressed genes across pseudotime
2.2.1 All genes
diff_test_res_all_genes <- differentialGeneTest(monocle,
fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
cores = 12,
num_clusters=1,
show_rownames = FALSE)
diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)2.2.2 Transcription factors
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())2.2.2.1 Pseudotime heatmaps of significant transcription factors
2.2.2.1.1 q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))## Number of significant genes: 4390significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))## Number of significant transcription factors: 260plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)## pdf
## 2heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Zfpm1 | -1.2712856 | -1.2592238 | -1.2468984 | -1.2343038 | -1.2214343 | -1.2082843 | -1.1948479 | -1.1811192 | -1.1670921 | -1.1527605 | -1.1381181 | -1.1231585 | -1.1078752 | -1.0922616 | -1.0763109 | -1.0600163 | -1.0433707 | -1.0263671 | -1.0089982 | -0.9912567 | -0.9731351 | -0.9546257 | -0.9357207 | -0.9164123 | -0.8966925 | -0.8765531 | -0.8559857 | -0.8349820 | -0.8135333 | -0.7916310 | -0.7692661 | -0.7464296 | -0.7231123 | -0.6993051 | -0.6749983 | -0.6501823 | -0.6248475 | -0.5989839 | -0.5725813 | -0.5456296 | -0.5181184 | -0.4900371 | -0.4613751 | -0.4321215 | -0.4022695 | -0.3718164 | -0.3407603 | -0.3090997 | -0.2768340 | -0.2439630 | -0.2104875 | -0.1764087 | -0.1417289 | -0.1064509 | -0.0705787 | -0.0341168 | 0.0029292 | 0.0405526 | 0.0787459 | 0.1175005 | 0.1568067 | 0.1966539 | 0.2370301 | 0.2779222 | 0.3193159 | 0.3611957 | 0.4035467 | 0.4463674 | 0.4896640 | 0.5334429 | 0.5777112 | 0.6224765 | 0.6677468 | 0.7135307 | 0.7598376 | 0.8066771 | 0.8540596 | 0.9019962 | 0.9504985 | 0.9995789 | 1.0492504 | 1.099527 | 1.150422 | 1.201952 | 1.254132 | 1.306980 | 1.360512 | 1.414748 | 1.469705 | 1.525406 | 1.581870 | 1.639120 | 1.697179 | 1.756071 | 1.815821 | 1.8764546 | 1.9380000 | 2.0004854 | 2.0639402 | 2.1283954 |
| Thra | -1.1413348 | -1.1296662 | -1.1179384 | -1.1061447 | -1.0942781 | -1.0823315 | -1.0702978 | -1.0581695 | -1.0459394 | -1.0335997 | -1.0211429 | -1.0085611 | -0.9958464 | -0.9829907 | -0.9699858 | -0.9568235 | -0.9434952 | -0.9299923 | -0.9163061 | -0.9024277 | -0.8883481 | -0.8740582 | -0.8595485 | -0.8448096 | -0.8298319 | -0.8146055 | -0.7991205 | -0.7833668 | -0.7673340 | -0.7510117 | -0.7343892 | -0.7174557 | -0.7002001 | -0.6826111 | -0.6646775 | -0.6463874 | -0.6277292 | -0.6086908 | -0.5892598 | -0.5694239 | -0.5491704 | -0.5284862 | -0.5073583 | -0.4857728 | -0.4637050 | -0.4411185 | -0.4179759 | -0.3942389 | -0.3698684 | -0.3448244 | -0.3190661 | -0.2925516 | -0.2652383 | -0.2370825 | -0.2080394 | -0.1780634 | -0.1471075 | -0.1151238 | -0.0820633 | -0.0478755 | -0.0125091 | 0.0240888 | 0.0619722 | 0.1011965 | 0.1418184 | 0.1838960 | 0.2274833 | 0.2725913 | 0.3192087 | 0.3673233 | 0.4169220 | 0.4679904 | 0.5205131 | 0.5744736 | 0.6298538 | 0.6866347 | 0.7447955 | 0.8043142 | 0.8651673 | 0.9273298 | 0.9907751 | 1.055475 | 1.121400 | 1.188519 | 1.256799 | 1.326205 | 1.396702 | 1.468252 | 1.540817 | 1.614354 | 1.688823 | 1.764181 | 1.840381 | 1.917379 | 1.995127 | 2.0735751 | 2.1526746 | 2.2323739 | 2.3126211 | 2.3933629 |
| Zfp579 | -0.7810556 | -0.7882617 | -0.7953880 | -0.8024058 | -0.8092868 | -0.8160039 | -0.8225304 | -0.8288404 | -0.8349087 | -0.8407104 | -0.8462215 | -0.8514181 | -0.8562766 | -0.8607738 | -0.8648867 | -0.8685922 | -0.8718672 | -0.8746884 | -0.8770323 | -0.8788748 | -0.8801914 | -0.8809569 | -0.8811451 | -0.8807290 | -0.8796802 | -0.8779689 | -0.8755640 | -0.8724324 | -0.8685389 | -0.8638462 | -0.8583146 | -0.8519013 | -0.8445604 | -0.8362429 | -0.8268957 | -0.8164615 | -0.8048785 | -0.7920798 | -0.7779927 | -0.7625387 | -0.7456323 | -0.7271808 | -0.7070830 | -0.6852317 | -0.6615676 | -0.6360868 | -0.6087878 | -0.5796703 | -0.5487360 | -0.5159894 | -0.4814388 | -0.4450975 | -0.4069842 | -0.3671247 | -0.3255522 | -0.2823090 | -0.2374465 | -0.1910271 | -0.1431246 | -0.0938250 | -0.0432274 | 0.0085550 | 0.0613950 | 0.1151501 | 0.1696626 | 0.2247594 | 0.2802654 | 0.3361074 | 0.3922668 | 0.4487271 | 0.5054737 | 0.5624937 | 0.6197763 | 0.6773126 | 0.7350960 | 0.7931216 | 0.8513870 | 0.9098916 | 0.9686373 | 1.0276280 | 1.0868700 | 1.146372 | 1.206143 | 1.266198 | 1.326552 | 1.387221 | 1.448225 | 1.509587 | 1.571331 | 1.633482 | 1.696071 | 1.759127 | 1.822684 | 1.886777 | 1.951445 | 2.0167275 | 2.0826663 | 2.1493062 | 2.2166940 | 2.2848790 |
| Zfp740 | -0.7565998 | -0.7659481 | -0.7752028 | -0.7843304 | -0.7932980 | -0.8020737 | -0.8106264 | -0.8189256 | -0.8269414 | -0.8346448 | -0.8420071 | -0.8490002 | -0.8555964 | -0.8617681 | -0.8674882 | -0.8727297 | -0.8774653 | -0.8816681 | -0.8853107 | -0.8883653 | -0.8908039 | -0.8925979 | -0.8937177 | -0.8941331 | -0.8938127 | -0.8927241 | -0.8908332 | -0.8881045 | -0.8845008 | -0.8799827 | -0.8745086 | -0.8680345 | -0.8605136 | -0.8518960 | -0.8421283 | -0.8311537 | -0.8189111 | -0.8053350 | -0.7903550 | -0.7738951 | -0.7558738 | -0.7362029 | -0.7147871 | -0.6915263 | -0.6663750 | -0.6393484 | -0.6104647 | -0.5797433 | -0.5472049 | -0.5128730 | -0.4767742 | -0.4389391 | -0.3994034 | -0.3582082 | -0.3154011 | -0.2710369 | -0.2251784 | -0.1778970 | -0.1292737 | -0.0793994 | -0.0283762 | 0.0236828 | 0.0766523 | 0.1303949 | 0.1847600 | 0.2395843 | 0.2947046 | 0.3500587 | 0.4056378 | 0.4614351 | 0.5174451 | 0.5736640 | 0.6300896 | 0.6867212 | 0.7435601 | 0.8006089 | 0.8578722 | 0.9153564 | 0.9730693 | 1.0310210 | 1.0892231 | 1.147689 | 1.206435 | 1.265477 | 1.324835 | 1.384531 | 1.444586 | 1.505027 | 1.565881 | 1.627176 | 1.688943 | 1.751216 | 1.814031 | 1.877423 | 1.941434 | 2.0061038 | 2.0714773 | 2.1376005 | 2.2045215 | 2.2722913 |
| Tmf1 | -0.6616883 | -0.6782612 | -0.6947307 | -0.7110485 | -0.7271672 | -0.7430397 | -0.7586198 | -0.7738616 | -0.7887199 | -0.8031500 | -0.8171077 | -0.8305492 | -0.8434311 | -0.8557102 | -0.8673439 | -0.8782894 | -0.8885045 | -0.8979467 | -0.9065738 | -0.9143435 | -0.9212131 | -0.9271401 | -0.9320813 | -0.9359934 | -0.9388325 | -0.9405539 | -0.9411124 | -0.9404620 | -0.9385556 | -0.9353451 | -0.9307812 | -0.9248133 | -0.9173893 | -0.9084555 | -0.8979563 | -0.8858343 | -0.8720299 | -0.8564813 | -0.8391243 | -0.8198918 | -0.7987141 | -0.7755182 | -0.7502281 | -0.7227671 | -0.6931308 | -0.6613905 | -0.6276212 | -0.5918985 | -0.5542992 | -0.5149015 | -0.4737853 | -0.4310327 | -0.3867283 | -0.3409593 | -0.2938159 | -0.2453916 | -0.1957836 | -0.1450925 | -0.0934230 | -0.0408838 | 0.0124121 | 0.0663475 | 0.1208005 | 0.1756451 | 0.2307503 | 0.2859808 | 0.3412081 | 0.3963916 | 0.4515355 | 0.5066448 | 0.5617250 | 0.6167820 | 0.6718224 | 0.7268530 | 0.7818815 | 0.8369157 | 0.8919640 | 0.9470356 | 1.0021396 | 1.0572862 | 1.1124855 | 1.167749 | 1.223087 | 1.278511 | 1.334035 | 1.389671 | 1.445431 | 1.501330 | 1.557382 | 1.613600 | 1.670001 | 1.726600 | 1.783412 | 1.840453 | 1.897741 | 1.9552933 | 2.0131266 | 2.0712595 | 2.1297105 | 2.1884986 |
| Tcf7l2 | -0.7576342 | -0.7685488 | -0.7793482 | -0.7899945 | -0.8004512 | -0.8106825 | -0.8206538 | -0.8303315 | -0.8396827 | -0.8486755 | -0.8572786 | -0.8654616 | -0.8731943 | -0.8804472 | -0.8871911 | -0.8933971 | -0.8990362 | -0.9040795 | -0.9084979 | -0.9122619 | -0.9153415 | -0.9177061 | -0.9193241 | -0.9201630 | -0.9201890 | -0.9193666 | -0.9176590 | -0.9150271 | -0.9114300 | -0.9068239 | -0.9011626 | -0.8943969 | -0.8864741 | -0.8773380 | -0.8669282 | -0.8551802 | -0.8420247 | -0.8273872 | -0.8111877 | -0.7933402 | -0.7737525 | -0.7523252 | -0.7289517 | -0.7035205 | -0.6759823 | -0.6463572 | -0.6146704 | -0.5809504 | -0.5452296 | -0.5075459 | -0.4679431 | -0.4264722 | -0.3831919 | -0.3381697 | -0.2914822 | -0.2432159 | -0.1934676 | -0.1423448 | -0.0899661 | -0.0364610 | 0.0180298 | 0.0733545 | 0.1293506 | 0.1858448 | 0.2426540 | 0.2995852 | 0.3564507 | 0.4131731 | 0.4697330 | 0.5261141 | 0.5823027 | 0.6382873 | 0.6940594 | 0.7496126 | 0.8049428 | 0.8600482 | 0.9149293 | 0.9695886 | 1.0240306 | 1.0782619 | 1.1322907 | 1.186127 | 1.239783 | 1.293273 | 1.346610 | 1.399813 | 1.452899 | 1.505887 | 1.558798 | 1.611656 | 1.664481 | 1.717301 | 1.770139 | 1.823023 | 1.875980 | 1.9290392 | 1.9822300 | 2.0355831 | 2.0891296 | 2.1429020 |
| Bbx | -0.9798442 | -0.9786615 | -0.9774545 | -0.9761993 | -0.9748721 | -0.9734489 | -0.9719057 | -0.9702186 | -0.9683632 | -0.9663155 | -0.9640509 | -0.9615450 | -0.9587732 | -0.9557106 | -0.9523320 | -0.9486124 | -0.9445259 | -0.9400469 | -0.9351490 | -0.9298056 | -0.9239899 | -0.9176741 | -0.9108305 | -0.9034303 | -0.8954444 | -0.8868428 | -0.8775951 | -0.8676697 | -0.8570344 | -0.8456558 | -0.8334998 | -0.8205309 | -0.8067127 | -0.7920071 | -0.7763750 | -0.7597757 | -0.7421669 | -0.7235046 | -0.7037430 | -0.6828342 | -0.6607285 | -0.6373738 | -0.6127157 | -0.5866988 | -0.5593054 | -0.5305577 | -0.5004803 | -0.4690984 | -0.4364381 | -0.4025264 | -0.3673916 | -0.3310635 | -0.2935734 | -0.2549544 | -0.2152417 | -0.1744723 | -0.1326857 | -0.0899239 | -0.0462313 | -0.0016553 | 0.0437540 | 0.0899434 | 0.1368566 | 0.1844340 | 0.2326127 | 0.2813262 | 0.3305104 | 0.3801469 | 0.4302402 | 0.4807951 | 0.5318168 | 0.5833105 | 0.6352815 | 0.6877352 | 0.7406774 | 0.7941140 | 0.8480508 | 0.9024941 | 0.9574503 | 1.0129257 | 1.0689272 | 1.125462 | 1.182536 | 1.240158 | 1.298334 | 1.357072 | 1.416381 | 1.476268 | 1.536741 | 1.597808 | 1.659480 | 1.721763 | 1.784668 | 1.848203 | 1.912378 | 1.9772033 | 2.0426880 | 2.1088426 | 2.1756774 | 2.2432031 |
| Tulp4 | -0.9739800 | -0.9756105 | -0.9772083 | -0.9787412 | -0.9801774 | -0.9814850 | -0.9826321 | -0.9835870 | -0.9843178 | -0.9847926 | -0.9849796 | -0.9848469 | -0.9843625 | -0.9834941 | -0.9822097 | -0.9804766 | -0.9782621 | -0.9755333 | -0.9722570 | -0.9683993 | -0.9639263 | -0.9588033 | -0.9529954 | -0.9464666 | -0.9391809 | -0.9311009 | -0.9221888 | -0.9124058 | -0.9017122 | -0.8900672 | -0.8774288 | -0.8637538 | -0.8489976 | -0.8331145 | -0.8160568 | -0.7977755 | -0.7782195 | -0.7573362 | -0.7350706 | -0.7113658 | -0.6861626 | -0.6593991 | -0.6310111 | -0.6009341 | -0.5691600 | -0.5357413 | -0.5007339 | -0.4641955 | -0.4261856 | -0.3867657 | -0.3459997 | -0.3039540 | -0.2606978 | -0.2163036 | -0.1708468 | -0.1244064 | -0.0770650 | -0.0289088 | 0.0199720 | 0.0694835 | 0.1195276 | 0.1700020 | 0.2208005 | 0.2718126 | 0.3229239 | 0.3740157 | 0.4249751 | 0.4757665 | 0.5263932 | 0.5768597 | 0.6271711 | 0.6773335 | 0.7273532 | 0.7772378 | 0.8269951 | 0.8766339 | 0.9261635 | 0.9755940 | 1.0249360 | 1.0742010 | 1.1234008 | 1.172548 | 1.221656 | 1.270739 | 1.319811 | 1.368887 | 1.417983 | 1.467115 | 1.516300 | 1.565555 | 1.614899 | 1.664349 | 1.713926 | 1.763648 | 1.813536 | 1.8636103 | 1.9138929 | 1.9644052 | 2.0151697 | 2.0662093 |
| Lcorl | 0.0145057 | -0.0450676 | -0.1034902 | -0.1606718 | -0.2165299 | -0.2709894 | -0.3239823 | -0.3754475 | -0.4253302 | -0.4735819 | -0.5201599 | -0.5650264 | -0.6081490 | -0.6494991 | -0.6890524 | -0.7267879 | -0.7626872 | -0.7967348 | -0.8289165 | -0.8592198 | -0.8876328 | -0.9141441 | -0.9387417 | -0.9614131 | -0.9821441 | -1.0009189 | -1.0177189 | -1.0325227 | -1.0453050 | -1.0560364 | -1.0646824 | -1.0712031 | -1.0755519 | -1.0776756 | -1.0775128 | -1.0749936 | -1.0700384 | -1.0625569 | -1.0524474 | -1.0395950 | -1.0238712 | -1.0051317 | -0.9832156 | -0.9579490 | -0.9292719 | -0.8972501 | -0.8619533 | -0.8234515 | -0.7818178 | -0.7371312 | -0.6894788 | -0.6389584 | -0.5856807 | -0.5297715 | -0.4713741 | -0.4106506 | -0.3477842 | -0.2829802 | -0.2164676 | -0.1484999 | -0.0793557 | -0.0093391 | 0.0612199 | 0.1319666 | 0.2025213 | 0.2724810 | 0.3414505 | 0.4092648 | 0.4758820 | 0.5412684 | 0.6053973 | 0.6682492 | 0.7298115 | 0.7900781 | 0.8490493 | 0.9067315 | 0.9631371 | 1.0182839 | 1.0721953 | 1.1248998 | 1.1764305 | 1.226825 | 1.276127 | 1.324382 | 1.371641 | 1.417957 | 1.463389 | 1.507999 | 1.551850 | 1.595010 | 1.637549 | 1.679541 | 1.721061 | 1.762187 | 1.803001 | 1.8435852 | 1.8840248 | 1.9244073 | 1.9648223 | 2.0053614 |
| Zfp516 | -0.2383464 | -0.2803540 | -0.3212084 | -0.3608676 | -0.3992963 | -0.4364655 | -0.4723517 | -0.5069366 | -0.5402064 | -0.5721515 | -0.6027659 | -0.6320468 | -0.6599939 | -0.6866091 | -0.7118961 | -0.7358599 | -0.7585066 | -0.7798424 | -0.7998741 | -0.8186078 | -0.8360493 | -0.8522033 | -0.8670733 | -0.8806608 | -0.8929655 | -0.9039848 | -0.9137129 | -0.9221412 | -0.9292575 | -0.9350453 | -0.9394839 | -0.9425477 | -0.9442052 | -0.9444192 | -0.9431457 | -0.9403330 | -0.9359213 | -0.9298415 | -0.9220145 | -0.9123496 | -0.9007435 | -0.8870787 | -0.8712221 | -0.8530263 | -0.8324120 | -0.8093782 | -0.7839222 | -0.7560386 | -0.7257204 | -0.6929614 | -0.6577579 | -0.6201110 | -0.5800283 | -0.5375268 | -0.4926346 | -0.4453935 | -0.3958615 | -0.3441153 | -0.2902525 | -0.2343947 | -0.1766893 | -0.1173122 | -0.0564698 | 0.0055993 | 0.0686220 | 0.1322906 | 0.1962851 | 0.2604586 | 0.3247586 | 0.3891368 | 0.4535486 | 0.5179535 | 0.5823152 | 0.6466016 | 0.7107854 | 0.7748440 | 0.8387596 | 0.9025194 | 0.9661159 | 1.0295464 | 1.0928139 | 1.155926 | 1.218897 | 1.281746 | 1.344496 | 1.407177 | 1.469824 | 1.532479 | 1.595187 | 1.658000 | 1.720975 | 1.784175 | 1.847668 | 1.911528 | 1.975835 | 2.0406741 | 2.1061368 | 2.1723202 | 2.2393276 | 2.3072684 |
| Dach2 | -0.2867327 | -0.3362488 | -0.3839235 | -0.4297318 | -0.4736593 | -0.5157015 | -0.5558619 | -0.5941516 | -0.6305879 | -0.6651935 | -0.6979954 | -0.7290238 | -0.7583118 | -0.7858941 | -0.8118067 | -0.8360857 | -0.8587673 | -0.8798866 | -0.8994775 | -0.9175719 | -0.9341994 | -0.9493866 | -0.9631570 | -0.9755302 | -0.9865214 | -0.9961415 | -1.0043957 | -1.0112839 | -1.0167995 | -1.0209289 | -1.0236513 | -1.0249369 | -1.0247471 | -1.0230329 | -1.0197338 | -1.0147765 | -1.0080734 | -0.9995208 | -0.9889968 | -0.9763587 | -0.9614404 | -0.9440490 | -0.9239608 | -0.9009215 | -0.8747562 | -0.8453882 | -0.8127374 | -0.7767192 | -0.7372485 | -0.6942445 | -0.6476353 | -0.5973637 | -0.5433927 | -0.4857124 | -0.4243463 | -0.3593585 | -0.2908616 | -0.2190235 | -0.1440755 | -0.0663186 | 0.0138692 | 0.0960280 | 0.1796115 | 0.2639843 | 0.3484210 | 0.4321079 | 0.5141978 | 0.5942034 | 0.6718484 | 0.7468826 | 0.8190823 | 0.8882513 | 0.9542217 | 1.0168544 | 1.0760389 | 1.1316932 | 1.1837632 | 1.2322219 | 1.2770683 | 1.3183262 | 1.3560429 | 1.390288 | 1.421150 | 1.448738 | 1.473177 | 1.494609 | 1.513187 | 1.529079 | 1.542461 | 1.553520 | 1.562450 | 1.569452 | 1.574730 | 1.578495 | 1.580959 | 1.5823369 | 1.5828447 | 1.5826999 | 1.5821200 | 1.5813227 |
| Mitf | -0.8963212 | -0.8989518 | -0.9015411 | -0.9040715 | -0.9065258 | -0.9088877 | -0.9111412 | -0.9132710 | -0.9152618 | -0.9170989 | -0.9187679 | -0.9202541 | -0.9215434 | -0.9226212 | -0.9234729 | -0.9240836 | -0.9244378 | -0.9245194 | -0.9243118 | -0.9237973 | -0.9229569 | -0.9217705 | -0.9202163 | -0.9182709 | -0.9159085 | -0.9131012 | -0.9098181 | -0.9060254 | -0.9016854 | -0.8967568 | -0.8911932 | -0.8849433 | -0.8779496 | -0.8701481 | -0.8614667 | -0.8518247 | -0.8411315 | -0.8292846 | -0.8161687 | -0.8016534 | -0.7855909 | -0.7678139 | -0.7481318 | -0.7263310 | -0.7022373 | -0.6757323 | -0.6466964 | -0.6150085 | -0.5805491 | -0.5432031 | -0.5028637 | -0.4594369 | -0.4128462 | -0.3630375 | -0.3099856 | -0.2536999 | -0.1942312 | -0.1316783 | -0.0661949 | 0.0020037 | 0.0726347 | 0.1453418 | 0.2196914 | 0.2951687 | 0.3711767 | 0.4470367 | 0.5220302 | 0.5957084 | 0.6677843 | 0.7379917 | 0.8060859 | 0.8718461 | 0.9350766 | 0.9956076 | 1.0532964 | 1.1080270 | 1.1597109 | 1.2082859 | 1.2537159 | 1.2959901 | 1.3351218 | 1.371147 | 1.404124 | 1.434129 | 1.461259 | 1.485627 | 1.507362 | 1.526604 | 1.543509 | 1.558241 | 1.570973 | 1.581889 | 1.591175 | 1.599027 | 1.605641 | 1.6112202 | 1.6159686 | 1.6200928 | 1.6238010 | 1.6273027 |
| Foxn3 | -0.5506148 | -0.5806278 | -0.6104213 | -0.6399189 | -0.6690452 | -0.6977267 | -0.7258907 | -0.7534663 | -0.7803837 | -0.8065741 | -0.8319701 | -0.8565051 | -0.8801135 | -0.9027305 | -0.9242921 | -0.9447348 | -0.9639956 | -0.9820117 | -0.9987206 | -1.0140599 | -1.0279668 | -1.0403784 | -1.0512313 | -1.0604615 | -1.0680039 | -1.0737926 | -1.0777603 | -1.0798382 | -1.0799558 | -1.0780405 | -1.0740178 | -1.0678103 | -1.0593380 | -1.0485179 | -1.0352636 | -1.0194848 | -1.0010875 | -0.9799729 | -0.9560379 | -0.9291738 | -0.8992666 | -0.8661962 | -0.8298361 | -0.7900593 | -0.7468848 | -0.7004864 | -0.6510473 | -0.5987545 | -0.5437996 | -0.4863798 | -0.4266989 | -0.3649682 | -0.3014072 | -0.2362438 | -0.1697156 | -0.1020699 | -0.0335642 | 0.0355335 | 0.1049448 | 0.1743803 | 0.2435402 | 0.3121141 | 0.3797816 | 0.4462123 | 0.5110668 | 0.5739971 | 0.6346766 | 0.6930123 | 0.7490306 | 0.8027632 | 0.8542465 | 0.9035209 | 0.9506310 | 0.9956253 | 1.0385555 | 1.0794772 | 1.1184491 | 1.1555327 | 1.1907926 | 1.2242959 | 1.2561124 | 1.286314 | 1.314975 | 1.342172 | 1.367981 | 1.392485 | 1.415762 | 1.437898 | 1.458974 | 1.479077 | 1.498294 | 1.516711 | 1.534418 | 1.551503 | 1.568057 | 1.5841706 | 1.5999354 | 1.6154437 | 1.6307885 | 1.6460631 |
| Ebf2 | -0.7522794 | -0.7534545 | -0.7545397 | -0.7555390 | -0.7564566 | -0.7572970 | -0.7580649 | -0.7587649 | -0.7594015 | -0.7599790 | -0.7605016 | -0.7609733 | -0.7613977 | -0.7617782 | -0.7621180 | -0.7624199 | -0.7626864 | -0.7629199 | -0.7631221 | -0.7632949 | -0.7634395 | -0.7635569 | -0.7636477 | -0.7637125 | -0.7637510 | -0.7637629 | -0.7637473 | -0.7637028 | -0.7636273 | -0.7635183 | -0.7633721 | -0.7631842 | -0.7629490 | -0.7626590 | -0.7623052 | -0.7618760 | -0.7613567 | -0.7607288 | -0.7599685 | -0.7590456 | -0.7579211 | -0.7565443 | -0.7548492 | -0.7527491 | -0.7501399 | -0.7468984 | -0.7428713 | -0.7378670 | -0.7316482 | -0.7239228 | -0.7143333 | -0.7024465 | -0.6877426 | -0.6696062 | -0.6473184 | -0.6200555 | -0.5868928 | -0.5468209 | -0.4987742 | -0.4416795 | -0.3745240 | -0.2964488 | -0.2068662 | -0.1055982 | 0.0069700 | 0.1297349 | 0.2608337 | 0.3984130 | 0.5406185 | 0.6853564 | 0.8303594 | 0.9732654 | 1.1117002 | 1.2433611 | 1.3660960 | 1.4779729 | 1.5773392 | 1.6628653 | 1.7335736 | 1.7888512 | 1.8284476 | 1.852459 | 1.861300 | 1.855669 | 1.836502 | 1.804928 | 1.762219 | 1.709743 | 1.648921 | 1.581181 | 1.507928 | 1.430513 | 1.350206 | 1.268181 | 1.185503 | 1.1031218 | 1.0218689 | 0.9424582 | 0.8654917 | 0.7914658 |
| Hmgxb3 | -1.1506975 | -1.1492093 | -1.1476889 | -1.1461063 | -1.1444311 | -1.1426326 | -1.1406801 | -1.1385424 | -1.1361882 | -1.1335856 | -1.1307024 | -1.1275056 | -1.1239620 | -1.1200374 | -1.1156967 | -1.1109042 | -1.1056227 | -1.0998140 | -1.0934386 | -1.0864552 | -1.0788210 | -1.0704910 | -1.0614182 | -1.0515531 | -1.0408435 | -1.0292341 | -1.0166665 | -1.0030785 | -0.9884037 | -0.9725716 | -0.9555064 | -0.9371271 | -0.9173465 | -0.8960709 | -0.8731994 | -0.8486229 | -0.8222237 | -0.7938740 | -0.7634356 | -0.7307582 | -0.6956786 | -0.6580190 | -0.6175860 | -0.5741733 | -0.5276835 | -0.4781472 | -0.4256117 | -0.3701387 | -0.3118070 | -0.2507156 | -0.1869868 | -0.1207692 | -0.0522406 | 0.0183892 | 0.0908759 | 0.1649378 | 0.2402541 | 0.3164635 | 0.3931622 | 0.4699041 | 0.5462007 | 0.6215217 | 0.6952971 | 0.7669196 | 0.8357486 | 0.9011150 | 0.9623703 | 1.0192178 | 1.0715586 | 1.1193244 | 1.1624757 | 1.2010008 | 1.2349150 | 1.2642591 | 1.2890977 | 1.3095180 | 1.3256281 | 1.3375549 | 1.3454424 | 1.3494500 | 1.3497506 | 1.346529 | 1.339978 | 1.330301 | 1.317707 | 1.302408 | 1.284622 | 1.264565 | 1.242458 | 1.218519 | 1.192963 | 1.166005 | 1.137854 | 1.108716 | 1.078792 | 1.0482775 | 1.0173617 | 0.9862282 | 0.9550542 | 0.9240108 |
| Zfp488 | -0.5745624 | -0.6086374 | -0.6421171 | -0.6749232 | -0.7069824 | -0.7382266 | -0.7685916 | -0.7980180 | -0.8264500 | -0.8538353 | -0.8801250 | -0.9052729 | -0.9292353 | -0.9519706 | -0.9734387 | -0.9936009 | -1.0124194 | -1.0298567 | -1.0458752 | -1.0604369 | -1.0735027 | -1.0850323 | -1.0949832 | -1.1033104 | -1.1099662 | -1.1148987 | -1.1180523 | -1.1193663 | -1.1187742 | -1.1162034 | -1.1115740 | -1.1047981 | -1.0957786 | -1.0844085 | -1.0705694 | -1.0541304 | -1.0349465 | -1.0128574 | -0.9876853 | -0.9592333 | -0.9272829 | -0.8915921 | -0.8518921 | -0.8078930 | -0.7594707 | -0.7066928 | -0.6496434 | -0.5884198 | -0.5231368 | -0.4539322 | -0.3809715 | -0.3044527 | -0.2246109 | -0.1417233 | -0.0561129 | 0.0318477 | 0.1217326 | 0.2130604 | 0.3052919 | 0.3978295 | 0.4900171 | 0.5811413 | 0.6704338 | 0.7570753 | 0.8402008 | 0.9189063 | 0.9923182 | 1.0600529 | 1.1220012 | 1.1780936 | 1.2282975 | 1.2726161 | 1.3110859 | 1.3437753 | 1.3707825 | 1.3922327 | 1.4082765 | 1.4190870 | 1.4248576 | 1.4257998 | 1.4221408 | 1.414121 | 1.401991 | 1.386012 | 1.366451 | 1.343580 | 1.317674 | 1.289009 | 1.257863 | 1.224508 | 1.189218 | 1.152259 | 1.113894 | 1.074379 | 1.033964 | 0.9928908 | 0.9513944 | 0.9097007 | 0.8680276 | 0.8265845 |
| Elf1 | -0.6961644 | -0.7208353 | -0.7449734 | -0.7685213 | -0.7914264 | -0.8136407 | -0.8351204 | -0.8558259 | -0.8757206 | -0.8947717 | -0.9129487 | -0.9302237 | -0.9465709 | -0.9619659 | -0.9763857 | -0.9898078 | -1.0022103 | -1.0135713 | -1.0238681 | -1.0330774 | -1.0411743 | -1.0481320 | -1.0539215 | -1.0585110 | -1.0618648 | -1.0639438 | -1.0647038 | -1.0640954 | -1.0620631 | -1.0585447 | -1.0534699 | -1.0467597 | -1.0383253 | -1.0280667 | -1.0158711 | -1.0016120 | -0.9851465 | -0.9663141 | -0.9449339 | -0.9208022 | -0.8936895 | -0.8633370 | -0.8294530 | -0.7917148 | -0.7499230 | -0.7040297 | -0.6539983 | -0.5998026 | -0.5414324 | -0.4789000 | -0.4122466 | -0.3415492 | -0.2669276 | -0.1885514 | -0.1066471 | -0.0215048 | 0.0665158 | 0.1569797 | 0.2493720 | 0.3430946 | 0.4374646 | 0.5317137 | 0.6249908 | 0.7163657 | 0.8048359 | 0.8893357 | 0.9688128 | 1.0427266 | 1.1108351 | 1.1729502 | 1.2289355 | 1.2787053 | 1.3222220 | 1.3594945 | 1.3905755 | 1.4155581 | 1.4345734 | 1.4477865 | 1.4553935 | 1.4576177 | 1.4547066 | 1.446928 | 1.434566 | 1.417921 | 1.397300 | 1.373021 | 1.345406 | 1.314779 | 1.281462 | 1.245779 | 1.208045 | 1.168571 | 1.127661 | 1.085609 | 1.042698 | 0.9992034 | 0.9553856 | 0.9114949 | 0.8677689 | 0.8244328 |
| Sox10 | -1.2928045 | -1.2824160 | -1.2719922 | -1.2615040 | -1.2509225 | -1.2402188 | -1.2293638 | -1.2183283 | -1.2070830 | -1.1955987 | -1.1838458 | -1.1717949 | -1.1594164 | -1.1466805 | -1.1335575 | -1.1200173 | -1.1060299 | -1.0915651 | -1.0765926 | -1.0610819 | -1.0450023 | -1.0283231 | -1.0110132 | -0.9930415 | -0.9743768 | -0.9549873 | -0.9348413 | -0.9139069 | -0.8921517 | -0.8695434 | -0.8460491 | -0.8216358 | -0.7962701 | -0.7699184 | -0.7425468 | -0.7141209 | -0.6846060 | -0.6539672 | -0.6221690 | -0.5891756 | -0.5549507 | -0.5194577 | -0.4826593 | -0.4445207 | -0.4050669 | -0.3643851 | -0.3225660 | -0.2797010 | -0.2358823 | -0.1912029 | -0.1457565 | -0.0996378 | -0.0529426 | -0.0057673 | 0.0417906 | 0.0896324 | 0.1376589 | 0.1857696 | 0.2338630 | 0.2818369 | 0.3295878 | 0.3770116 | 0.4240030 | 0.4704562 | 0.5162641 | 0.5613191 | 0.6055229 | 0.6488580 | 0.6913474 | 0.7330146 | 0.7738835 | 0.8139783 | 0.8533237 | 0.8919444 | 0.9298658 | 0.9671133 | 1.0037127 | 1.0396900 | 1.0750716 | 1.1098841 | 1.1441543 | 1.177909 | 1.211176 | 1.243983 | 1.276356 | 1.308326 | 1.339918 | 1.371162 | 1.402086 | 1.432719 | 1.463089 | 1.493226 | 1.523159 | 1.552917 | 1.582530 | 1.6120274 | 1.6414388 | 1.6707944 | 1.7001242 | 1.7294585 |
| Zeb2 | -0.7180968 | -0.7410789 | -0.7637920 | -0.7861678 | -0.8081402 | -0.8296457 | -0.8506229 | -0.8710128 | -0.8907581 | -0.9098038 | -0.9280965 | -0.9455843 | -0.9622168 | -0.9779447 | -0.9927197 | -1.0064942 | -1.0192211 | -1.0308534 | -1.0413441 | -1.0506457 | -1.0587101 | -1.0654881 | -1.0709290 | -1.0749806 | -1.0775882 | -1.0786947 | -1.0782402 | -1.0761611 | -1.0723899 | -1.0668549 | -1.0594791 | -1.0501804 | -1.0388703 | -1.0254538 | -1.0098284 | -0.9918835 | -0.9714999 | -0.9485487 | -0.9228907 | -0.8943754 | -0.8628403 | -0.8281098 | -0.7899945 | -0.7482966 | -0.7029642 | -0.6541077 | -0.6018543 | -0.5463430 | -0.4877279 | -0.4261797 | -0.3618885 | -0.2950656 | -0.2259447 | -0.1547834 | -0.0818642 | -0.0074949 | 0.0679911 | 0.1442351 | 0.2208534 | 0.2974382 | 0.3735591 | 0.4487640 | 0.5225817 | 0.5945233 | 0.6640846 | 0.7307491 | 0.7940291 | 0.8537544 | 0.9099226 | 0.9625474 | 1.0116557 | 1.0572871 | 1.0994927 | 1.1383342 | 1.1738831 | 1.2062196 | 1.2354319 | 1.2616158 | 1.2848734 | 1.3053128 | 1.3230474 | 1.338195 | 1.350879 | 1.361224 | 1.369360 | 1.375417 | 1.379532 | 1.381838 | 1.382475 | 1.381580 | 1.379293 | 1.375756 | 1.371108 | 1.365490 | 1.359044 | 1.3519102 | 1.3442293 | 1.3361413 | 1.3277859 | 1.3193019 |
| Zfp276 | -0.9059086 | -0.9172381 | -0.9284397 | -0.9394636 | -0.9502611 | -0.9607851 | -0.9709894 | -0.9808291 | -0.9902602 | -0.9992398 | -1.0077254 | -1.0156754 | -1.0230488 | -1.0298045 | -1.0359021 | -1.0413007 | -1.0459594 | -1.0498369 | -1.0528911 | -1.0550792 | -1.0563569 | -1.0566790 | -1.0559982 | -1.0542653 | -1.0514290 | -1.0474349 | -1.0422259 | -1.0357414 | -1.0279167 | -1.0186829 | -1.0079663 | -0.9956877 | -0.9817616 | -0.9660963 | -0.9485922 | -0.9291417 | -0.9076282 | -0.8839248 | -0.8578936 | -0.8293845 | -0.7982337 | -0.7642625 | -0.7272754 | -0.6870646 | -0.6435442 | -0.5967682 | -0.5468040 | -0.4937295 | -0.4376359 | -0.3786301 | -0.3168382 | -0.2524079 | -0.1855115 | -0.1163484 | -0.0451477 | 0.0278295 | 0.1022882 | 0.1778973 | 0.2542890 | 0.3310572 | 0.4077577 | 0.4839079 | 0.5589884 | 0.6324443 | 0.7036876 | 0.7721008 | 0.8370833 | 0.8983692 | 0.9558771 | 1.0095489 | 1.0593471 | 1.1052551 | 1.1472762 | 1.1854326 | 1.2197645 | 1.2503292 | 1.2771999 | 1.3004649 | 1.3202257 | 1.3365966 | 1.3497030 | 1.359681 | 1.366674 | 1.370834 | 1.372322 | 1.371300 | 1.367939 | 1.362409 | 1.354888 | 1.345551 | 1.334577 | 1.322143 | 1.308429 | 1.293611 | 1.277865 | 1.2613647 | 1.2442824 | 1.2267874 | 1.2090464 | 1.1912235 |
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.2 Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=TRUE, return_matrix = TRUE)
ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_5_10_minus_5, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_differential_gene_test_analysis_qval_5_10_minus_5_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.3 q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))## Number of significant genes: 6428significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))## Number of significant transcription factors: 428plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)## pdf
## 2heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Zkscan1 | -2.3515088 | -2.2867933 | -2.2213874 | -2.1553217 | -2.0886285 | -2.0213417 | -1.9534967 | -1.8851308 | -1.8162828 | -1.7469932 | -1.6773043 | -1.6072600 | -1.5369059 | -1.4662894 | -1.3954596 | -1.3244672 | -1.2533647 | -1.1822062 | -1.1110476 | -1.0399464 | -0.9689616 | -0.8981540 | -0.8275857 | -0.7573205 | -0.6874238 | -0.6179622 | -0.5490038 | -0.4806181 | -0.4128757 | -0.3458487 | -0.2796101 | -0.2142342 | -0.1497961 | -0.0863721 | -0.0240392 | 0.0371249 | 0.0970416 | 0.1556318 | 0.2128160 | 0.2685141 | 0.3226458 | 0.3751307 | 0.4258881 | 0.4748383 | 0.5219180 | 0.5670820 | 0.6102866 | 0.6514890 | 0.6906476 | 0.7277220 | 0.7626730 | 0.7954622 | 0.8260531 | 0.8544099 | 0.8804984 | 0.9042860 | 0.9257411 | 0.9448340 | 0.9615361 | 0.9758207 | 0.9876625 | 0.9970380 | 1.0039252 | 1.0083040 | 1.0101559 | 1.0094643 | 1.0062213 | 1.0004773 | 0.9923120 | 0.9818066 | 0.9690438 | 0.9541073 | 0.9370819 | 0.9180530 | 0.8971068 | 0.8743300 | 0.8498096 | 0.8236329 | 0.7958872 | 0.7666599 | 0.7360382 | 0.7041089 | 0.6709587 | 0.6366736 | 0.6013392 | 0.5650403 | 0.5278612 | 0.4898850 | 0.4511944 | 0.4118708 | 0.3719947 | 0.3316457 | 0.2909020 | 0.2498409 | 0.2085385 | 0.1670696 | 0.1255078 | 0.0839255 | 0.0423939 | 0.0009829 |
| Tcf25 | -2.0686885 | -2.0166078 | -1.9643685 | -1.9119697 | -1.8594107 | -1.8066909 | -1.7538093 | -1.7007653 | -1.6475582 | -1.5941871 | -1.5406512 | -1.4869498 | -1.4330822 | -1.3790474 | -1.3248448 | -1.2704735 | -1.2159327 | -1.1612216 | -1.1063394 | -1.0512853 | -0.9960584 | -0.9406580 | -0.8850831 | -0.8293329 | -0.7734066 | -0.7173034 | -0.6610223 | -0.6045626 | -0.5479233 | -0.4911035 | -0.4341025 | -0.3769192 | -0.3195529 | -0.2620025 | -0.2042673 | -0.1463463 | -0.0882386 | -0.0299433 | 0.0285406 | 0.0872139 | 0.1460777 | 0.2051327 | 0.2643801 | 0.3238164 | 0.3833340 | 0.4427179 | 0.5017458 | 0.5601929 | 0.6178324 | 0.6744349 | 0.7297693 | 0.7836021 | 0.8356982 | 0.8858208 | 0.9337316 | 0.9791912 | 1.0219589 | 1.0617935 | 1.0984533 | 1.1316965 | 1.1612814 | 1.1869669 | 1.2085129 | 1.2256805 | 1.2382327 | 1.2459345 | 1.2485826 | 1.2462116 | 1.2389742 | 1.2270272 | 1.2105296 | 1.1896430 | 1.1645310 | 1.1353589 | 1.1022934 | 1.0655026 | 1.0251553 | 0.9814213 | 0.9344707 | 0.8844736 | 0.8316007 | 0.7760219 | 0.7179071 | 0.6574256 | 0.5947459 | 0.5300354 | 0.4634607 | 0.3951872 | 0.3253788 | 0.2541979 | 0.1818056 | 0.1083609 | 0.0340213 | -0.0410575 | -0.1167220 | -0.1928205 | -0.2692035 | -0.3457234 | -0.4222350 | -0.4985949 |
| Mxd4 | -2.4702821 | -2.4059614 | -2.3401159 | -2.2727727 | -2.2039639 | -2.1337271 | -2.0621056 | -1.9891483 | -1.9149102 | -1.8394525 | -1.7628427 | -1.6851547 | -1.6064690 | -1.5268730 | -1.4464607 | -1.3653327 | -1.2835966 | -1.2013669 | -1.1187645 | -1.0359171 | -0.9529591 | -0.8700310 | -0.7872795 | -0.7048575 | -0.6229234 | -0.5416410 | -0.4611795 | -0.3817125 | -0.3034183 | -0.2264788 | -0.1510797 | -0.0774097 | -0.0056598 | 0.0639768 | 0.1313054 | 0.1961307 | 0.2582568 | 0.3174886 | 0.3736317 | 0.4264934 | 0.4758835 | 0.5216148 | 0.5635039 | 0.6013779 | 0.6352150 | 0.6651509 | 0.6913389 | 0.7139418 | 0.7331311 | 0.7490859 | 0.7619920 | 0.7720408 | 0.7794286 | 0.7843559 | 0.7870263 | 0.7876463 | 0.7864242 | 0.7835696 | 0.7792932 | 0.7738061 | 0.7673194 | 0.7600440 | 0.7521902 | 0.7439675 | 0.7355846 | 0.7272492 | 0.7191519 | 0.7113486 | 0.7038304 | 0.6965876 | 0.6896109 | 0.6828908 | 0.6764180 | 0.6701832 | 0.6641772 | 0.6583909 | 0.6528151 | 0.6474408 | 0.6422589 | 0.6372605 | 0.6324367 | 0.6277785 | 0.6232770 | 0.6189234 | 0.6147090 | 0.6106250 | 0.6066626 | 0.6028131 | 0.5990677 | 0.5954180 | 0.5918551 | 0.5883705 | 0.5849556 | 0.5816017 | 0.5783004 | 0.5750431 | 0.5718212 | 0.5686262 | 0.5654497 | 0.5622831 |
| Sox4 | -2.3108759 | -2.2496594 | -2.1877902 | -2.1253049 | -2.0622417 | -1.9986405 | -1.9345429 | -1.8699918 | -1.8050321 | -1.7397101 | -1.6740734 | -1.6081714 | -1.5420548 | -1.4757756 | -1.4093872 | -1.3429444 | -1.2765031 | -1.2101204 | -1.1438546 | -1.0777649 | -1.0119118 | -0.9463565 | -0.8811612 | -0.8163888 | -0.7521030 | -0.6883683 | -0.6252497 | -0.5628129 | -0.5011240 | -0.4402495 | -0.3802564 | -0.3212119 | -0.2631836 | -0.2062391 | -0.1504462 | -0.0958728 | -0.0425869 | 0.0093439 | 0.0598517 | 0.1088691 | 0.1563286 | 0.2021632 | 0.2463064 | 0.2886934 | 0.3293009 | 0.3681482 | 0.4052581 | 0.4406545 | 0.4743631 | 0.5064104 | 0.5368245 | 0.5656343 | 0.5928700 | 0.6185627 | 0.6427444 | 0.6654479 | 0.6867071 | 0.7065564 | 0.7250309 | 0.7421667 | 0.7580001 | 0.7725683 | 0.7859088 | 0.7980597 | 0.8090597 | 0.8189475 | 0.8277619 | 0.8355356 | 0.8422987 | 0.8480814 | 0.8529145 | 0.8568286 | 0.8598549 | 0.8620244 | 0.8633686 | 0.8639191 | 0.8637074 | 0.8627654 | 0.8611249 | 0.8588180 | 0.8558766 | 0.8523330 | 0.8482191 | 0.8435674 | 0.8384098 | 0.8327788 | 0.8267064 | 0.8202249 | 0.8133665 | 0.8061634 | 0.7986477 | 0.7908515 | 0.7828068 | 0.7745456 | 0.7660999 | 0.7575015 | 0.7487822 | 0.7399737 | 0.7311077 | 0.7222157 |
| Mycl | -0.8139043 | -0.8356217 | -0.8570808 | -0.8781969 | -0.8988877 | -0.9190737 | -0.9386780 | -0.9576256 | -0.9758441 | -0.9932627 | -1.0098125 | -1.0254258 | -1.0400364 | -1.0535788 | -1.0659880 | -1.0771995 | -1.0871484 | -1.0957695 | -1.1029965 | -1.1087619 | -1.1129964 | -1.1156284 | -1.1165834 | -1.1157837 | -1.1131477 | -1.1085892 | -1.1020169 | -1.0933336 | -1.0824355 | -1.0692114 | -1.0535420 | -1.0352986 | -1.0143426 | -0.9905241 | -0.9636813 | -0.9336384 | -0.9002053 | -0.8631758 | -0.8223259 | -0.7774128 | -0.7281729 | -0.6743200 | -0.6155438 | -0.5515192 | -0.4821733 | -0.4077212 | -0.3284172 | -0.2445489 | -0.1564421 | -0.0644661 | 0.0309624 | 0.1293757 | 0.2302525 | 0.3330160 | 0.4370333 | 0.5416155 | 0.6460186 | 0.7494465 | 0.8510536 | 0.9499494 | 1.0452041 | 1.1358542 | 1.2209101 | 1.2993640 | 1.3701986 | 1.4323966 | 1.4850304 | 1.5278494 | 1.5609704 | 1.5845620 | 1.5988387 | 1.6040561 | 1.6005069 | 1.5885170 | 1.5684413 | 1.5406606 | 1.5055775 | 1.4636133 | 1.4152045 | 1.3607999 | 1.3008575 | 1.2358413 | 1.1662188 | 1.0924581 | 1.0150253 | 0.9343821 | 0.8509834 | 0.7652750 | 0.6776917 | 0.5886550 | 0.4985718 | 0.4078323 | 0.3168090 | 0.2258555 | 0.1353050 | 0.0454702 | -0.0433578 | -0.1309095 | -0.2169374 | -0.3012157 |
| Zfp809 | -1.3034221 | -1.2958219 | -1.2881296 | -1.2803221 | -1.2723759 | -1.2642664 | -1.2559680 | -1.2474542 | -1.2386977 | -1.2296698 | -1.2203409 | -1.2106801 | -1.2006551 | -1.1902322 | -1.1793763 | -1.1680504 | -1.1562159 | -1.1438322 | -1.1308565 | -1.1172436 | -1.1029460 | -1.0879132 | -1.0720919 | -1.0554255 | -1.0378535 | -1.0193120 | -0.9997324 | -0.9790415 | -0.9571613 | -0.9340078 | -0.9094910 | -0.8835142 | -0.8559734 | -0.8267563 | -0.7957420 | -0.7627996 | -0.7277877 | -0.6905529 | -0.6509291 | -0.6087355 | -0.5637761 | -0.5158371 | -0.4646857 | -0.4100742 | -0.3518881 | -0.2901735 | -0.2250053 | -0.1564849 | -0.0847443 | -0.0099508 | 0.0676884 | 0.1479223 | 0.2304514 | 0.3149246 | 0.4009352 | 0.4880187 | 0.5756506 | 0.6632457 | 0.7501580 | 0.8356825 | 0.9190582 | 0.9994720 | 1.0760662 | 1.1479455 | 1.2141879 | 1.2738564 | 1.3260735 | 1.3704829 | 1.4070306 | 1.4357279 | 1.4566478 | 1.4699204 | 1.4757293 | 1.4743068 | 1.4659285 | 1.4509085 | 1.4295937 | 1.4023585 | 1.3695993 | 1.3317295 | 1.2891742 | 1.2423656 | 1.1917382 | 1.1377253 | 1.0807546 | 1.0212450 | 0.9596041 | 0.8962250 | 0.8314846 | 0.7657416 | 0.6993355 | 0.6325851 | 0.5657882 | 0.4992210 | 0.4331382 | 0.3677731 | 0.3033378 | 0.2400242 | 0.1780042 | 0.1174311 |
| Hif1a | -0.3962246 | -0.4416984 | -0.4867114 | -0.5311344 | -0.5748421 | -0.6177130 | -0.6596289 | -0.7004752 | -0.7401405 | -0.7785164 | -0.8154974 | -0.8509803 | -0.8848643 | -0.9170506 | -0.9474418 | -0.9759420 | -1.0024560 | -1.0268890 | -1.0491466 | -1.0691335 | -1.0867540 | -1.1019108 | -1.1145047 | -1.1244341 | -1.1315946 | -1.1358778 | -1.1371715 | -1.1353584 | -1.1303155 | -1.1219136 | -1.1100165 | -1.0944800 | -1.0751511 | -1.0518673 | -1.0244552 | -0.9927300 | -0.9564943 | -0.9155368 | -0.8696312 | -0.8185352 | -0.7619888 | -0.6997133 | -0.6314097 | -0.5567727 | -0.4758483 | -0.3890663 | -0.2968956 | -0.1998325 | -0.0984055 | 0.0068214 | 0.1152451 | 0.2262212 | 0.3390618 | 0.4530350 | 0.5673641 | 0.6812284 | 0.7937644 | 0.9040680 | 1.0111974 | 1.1141771 | 1.2120022 | 1.3036439 | 1.3880557 | 1.4641802 | 1.5309570 | 1.5873308 | 1.6323521 | 1.6658479 | 1.6880540 | 1.6992512 | 1.6997592 | 1.6899327 | 1.6701572 | 1.6408462 | 1.6024371 | 1.5553878 | 1.5001742 | 1.4372860 | 1.3672246 | 1.2904995 | 1.2076262 | 1.1191228 | 1.0255078 | 0.9272976 | 0.8250042 | 0.7191327 | 0.6101798 | 0.4986311 | 0.3849599 | 0.2696254 | 0.1530710 | 0.0357232 | -0.0820095 | -0.1997379 | -0.3170925 | -0.4337244 | -0.5493056 | -0.6635294 | -0.7761102 | -0.8867837 |
| Hmg20b | -0.1945130 | -0.2543854 | -0.3136301 | -0.3721075 | -0.4296825 | -0.4862246 | -0.5416075 | -0.5957090 | -0.6484108 | -0.6995982 | -0.7491600 | -0.7969880 | -0.8429768 | -0.8870234 | -0.9290272 | -0.9688890 | -1.0065113 | -1.0417975 | -1.0746514 | -1.1049772 | -1.1326787 | -1.1576589 | -1.1798194 | -1.1990603 | -1.2152791 | -1.2283706 | -1.2382259 | -1.2447321 | -1.2477717 | -1.2472215 | -1.2429524 | -1.2348281 | -1.2227049 | -1.2064301 | -1.1858419 | -1.1607679 | -1.1310242 | -1.0964144 | -1.0567282 | -1.0117406 | -0.9612101 | -0.9048773 | -0.8424637 | -0.7736845 | -0.6985871 | -0.6175776 | -0.5310916 | -0.4395830 | -0.3435273 | -0.2434260 | -0.1398097 | -0.0332408 | 0.0756840 | 0.1863317 | 0.2980314 | 0.4100739 | 0.5217112 | 0.6321570 | 0.7405878 | 0.8461449 | 0.9479367 | 1.0450428 | 1.1365173 | 1.2213947 | 1.2986956 | 1.3674330 | 1.4267031 | 1.4762919 | 1.5163489 | 1.5470597 | 1.5686421 | 1.5813426 | 1.5854345 | 1.5812147 | 1.5690013 | 1.5491311 | 1.5219568 | 1.4878448 | 1.4471725 | 1.4003263 | 1.3476992 | 1.2896886 | 1.2266947 | 1.1591181 | 1.0873583 | 1.0118121 | 0.9328719 | 0.8509246 | 0.7663500 | 0.6795201 | 0.5907975 | 0.5005351 | 0.4090752 | 0.3167489 | 0.2238752 | 0.1307614 | 0.0377022 | -0.0550202 | -0.1471362 | -0.2383887 |
| Atf6b | -0.2376819 | -0.2951443 | -0.3520373 | -0.4082242 | -0.4635723 | -0.5179530 | -0.5712416 | -0.6233173 | -0.6740626 | -0.7233634 | -0.7711090 | -0.8171912 | -0.8615045 | -0.9039458 | -0.9444138 | -0.9828091 | -1.0190334 | -1.0529895 | -1.0845805 | -1.1137099 | -1.1402807 | -1.1641955 | -1.1853554 | -1.2036600 | -1.2190067 | -1.2312901 | -1.2404017 | -1.2462289 | -1.2486551 | -1.2475581 | -1.2428103 | -1.2342774 | -1.2218181 | -1.2052828 | -1.1845135 | -1.1593420 | -1.1295897 | -1.0950664 | -1.0555690 | -1.0108809 | -0.9607701 | -0.9049887 | -0.8432710 | -0.7753467 | -0.7012697 | -0.6214432 | -0.5362991 | -0.4462861 | -0.3518735 | -0.2535547 | -0.1518499 | -0.0473088 | 0.0594877 | 0.1679256 | 0.2773566 | 0.3870977 | 0.4964312 | 0.6046050 | 0.7108342 | 0.8143021 | 0.9141633 | 1.0095467 | 1.0995588 | 1.1832886 | 1.2598123 | 1.3281996 | 1.3875982 | 1.4378123 | 1.4789889 | 1.5113074 | 1.5349745 | 1.5502220 | 1.5573049 | 1.5564985 | 1.5480968 | 1.5324098 | 1.5097617 | 1.4804887 | 1.4449368 | 1.4034603 | 1.3564198 | 1.3041801 | 1.2471089 | 1.1855752 | 1.1199475 | 1.0505929 | 0.9778752 | 0.9021542 | 0.8237844 | 0.7431139 | 0.6604838 | 0.5762273 | 0.4906686 | 0.4041230 | 0.3168959 | 0.2292827 | 0.1415683 | 0.0540270 | -0.0330777 | -0.1194930 |
| Xpa | -1.7642787 | -1.7247771 | -1.6848583 | -1.6445148 | -1.6037387 | -1.5625222 | -1.5208571 | -1.4787351 | -1.4361478 | -1.3930864 | -1.3495421 | -1.3055058 | -1.2609680 | -1.2159194 | -1.1703502 | -1.1242505 | -1.0776099 | -1.0304183 | -0.9826648 | -0.9343387 | -0.8854288 | -0.8359237 | -0.7858118 | -0.7350813 | -0.6837200 | -0.6317154 | -0.5790550 | -0.5257256 | -0.4717142 | -0.4170072 | -0.3615907 | -0.3054506 | -0.2485725 | -0.1909416 | -0.1325429 | -0.0733609 | -0.0133800 | 0.0474159 | 0.1090432 | 0.1715186 | 0.2348593 | 0.2990828 | 0.3642069 | 0.4302435 | 0.4970532 | 0.5643342 | 0.6317648 | 0.6990103 | 0.7657228 | 0.8315415 | 0.8960935 | 0.9589942 | 1.0198479 | 1.0782494 | 1.1337848 | 1.1860328 | 1.2345672 | 1.2789576 | 1.3187726 | 1.3535811 | 1.3829555 | 1.4064740 | 1.4237235 | 1.4343029 | 1.4378258 | 1.4339241 | 1.4222961 | 1.4030296 | 1.3764124 | 1.3427524 | 1.3023736 | 1.2556138 | 1.2028220 | 1.1443564 | 1.0805820 | 1.0118685 | 0.9385882 | 0.8611139 | 0.7798174 | 0.6950674 | 0.6072283 | 0.5166583 | 0.4237082 | 0.3287202 | 0.2320268 | 0.1339497 | 0.0347992 | -0.0651270 | -0.1655437 | -0.2661795 | -0.3667764 | -0.4670906 | -0.5668925 | -0.6659665 | -0.7641115 | -0.8611402 | -0.9568791 | -1.0511685 | -1.1438616 | -1.2348247 |
| Xbp1 | -1.6987856 | -1.6575967 | -1.6160776 | -1.5742199 | -1.5320153 | -1.4894551 | -1.4465305 | -1.4032324 | -1.3595517 | -1.3154787 | -1.2710039 | -1.2261174 | -1.1808090 | -1.1350685 | -1.0888851 | -1.0422482 | -0.9951467 | -0.9475694 | -0.8995046 | -0.8509408 | -0.8018658 | -0.7522674 | -0.7021331 | -0.6514501 | -0.6002054 | -0.5483856 | -0.4959771 | -0.4429661 | -0.3893385 | -0.3350797 | -0.2801750 | -0.2246094 | -0.1683676 | -0.1114338 | -0.0537921 | 0.0045737 | 0.0636804 | 0.1235448 | 0.1841843 | 0.2456164 | 0.3078592 | 0.3709310 | 0.4348505 | 0.4996299 | 0.5651170 | 0.6309852 | 0.6968898 | 0.7624755 | 0.8273761 | 0.8912156 | 0.9536078 | 1.0141577 | 1.0724615 | 1.1281082 | 1.1806803 | 1.2297553 | 1.2749068 | 1.3157066 | 1.3517257 | 1.3825370 | 1.4077168 | 1.4268473 | 1.4395187 | 1.4453320 | 1.4439014 | 1.4348573 | 1.4178950 | 1.3931090 | 1.3607960 | 1.3212696 | 1.2748564 | 1.2218942 | 1.1627302 | 1.0977189 | 1.0272208 | 0.9516001 | 0.8712233 | 0.7864577 | 0.6976696 | 0.6052232 | 0.5094790 | 0.4107927 | 0.3095138 | 0.2059848 | 0.1005398 | -0.0064959 | -0.1148071 | -0.2240891 | -0.3340486 | -0.4444039 | -0.5548858 | -0.6652373 | -0.7752147 | -0.8845870 | -0.9931365 | -1.1006586 | -1.2069618 | -1.3118675 | -1.4152101 | -1.5168362 |
| Nkx2-2 | -0.0138960 | -0.0719516 | -0.1290422 | -0.1850259 | -0.2397697 | -0.2931491 | -0.3450476 | -0.3953569 | -0.4439760 | -0.4908108 | -0.5357738 | -0.5787834 | -0.6197628 | -0.6586404 | -0.6953478 | -0.7298202 | -0.7619948 | -0.7918103 | -0.8192061 | -0.8441214 | -0.8664939 | -0.8862594 | -0.9033505 | -0.9176957 | -0.9292179 | -0.9378340 | -0.9434531 | -0.9459754 | -0.9452910 | -0.9412786 | -0.9338037 | -0.9227173 | -0.9078538 | -0.8890300 | -0.8660424 | -0.8386654 | -0.8066495 | -0.7697182 | -0.7275665 | -0.6798574 | -0.6262199 | -0.5662457 | -0.4994865 | -0.4254684 | -0.3440988 | -0.2557248 | -0.1607588 | -0.0596711 | 0.0470004 | 0.1586416 | 0.2745562 | 0.3939607 | 0.5159821 | 0.6396572 | 0.7639348 | 0.8876788 | 1.0096744 | 1.1286355 | 1.2432141 | 1.3520111 | 1.4535881 | 1.5464812 | 1.6292145 | 1.7003161 | 1.7583342 | 1.8018538 | 1.8296376 | 1.8415190 | 1.8379103 | 1.8193148 | 1.7863146 | 1.7395623 | 1.6797741 | 1.6077224 | 1.5242290 | 1.4301588 | 1.3264133 | 1.2139237 | 1.0936449 | 0.9665481 | 0.8336139 | 0.6958249 | 0.5541582 | 0.4095775 | 0.2630253 | 0.1154148 | -0.0323774 | -0.1795193 | -0.3252300 | -0.4687863 | -0.6095277 | -0.7468612 | -0.8802645 | -1.0092875 | -1.1335539 | -1.2527598 | -1.3666724 | -1.4751270 | -1.5780226 | -1.6753178 |
| Son | -0.2791494 | -0.3271638 | -0.3749621 | -0.4223987 | -0.4693291 | -0.5156097 | -0.5610975 | -0.6056504 | -0.6491271 | -0.6913869 | -0.7322900 | -0.7716969 | -0.8094689 | -0.8454678 | -0.8795555 | -0.9115946 | -0.9414478 | -0.9689779 | -0.9940478 | -1.0165202 | -1.0362578 | -1.0531228 | -1.0669770 | -1.0776817 | -1.0850973 | -1.0890834 | -1.0894986 | -1.0862001 | -1.0790439 | -1.0678843 | -1.0525739 | -1.0329633 | -1.0089011 | -0.9802334 | -0.9468040 | -0.9084536 | -0.8650204 | -0.8163391 | -0.7622412 | -0.7025546 | -0.6371035 | -0.5657079 | -0.4881838 | -0.4043606 | -0.3144901 | -0.2192615 | -0.1193895 | -0.0155967 | 0.0913862 | 0.2008196 | 0.3119543 | 0.4240314 | 0.5362824 | 0.6479289 | 0.7581832 | 0.8662484 | 0.9713192 | 1.0725824 | 1.1692180 | 1.2604000 | 1.3452976 | 1.4230765 | 1.4929001 | 1.5539315 | 1.6053346 | 1.6462763 | 1.6760144 | 1.6945180 | 1.7021106 | 1.6991270 | 1.6859108 | 1.6628128 | 1.6301907 | 1.5884081 | 1.5378336 | 1.4788405 | 1.4118057 | 1.3371093 | 1.2551338 | 1.1662637 | 1.0708847 | 0.9693832 | 0.8621460 | 0.7495593 | 0.6320086 | 0.5098782 | 0.3835503 | 0.2534050 | 0.1198197 | -0.0168312 | -0.1561771 | -0.2978511 | -0.4414906 | -0.5867377 | -0.7332392 | -0.8806474 | -1.0286199 | -1.1768200 | -1.3249170 | -1.4725862 |
| Sox8 | -0.5141742 | -0.5439075 | -0.5733761 | -0.6024667 | -0.6310684 | -0.6590726 | -0.6863728 | -0.7128645 | -0.7384452 | -0.7630142 | -0.7864723 | -0.8087217 | -0.8296657 | -0.8492088 | -0.8672559 | -0.8837125 | -0.8984839 | -0.9114755 | -0.9225918 | -0.9317365 | -0.9388119 | -0.9437185 | -0.9463546 | -0.9466156 | -0.9443941 | -0.9395788 | -0.9320540 | -0.9216996 | -0.9083899 | -0.8919931 | -0.8723712 | -0.8493785 | -0.8228615 | -0.7926582 | -0.7585969 | -0.7204958 | -0.6781623 | -0.6313921 | -0.5799680 | -0.5236597 | -0.4622226 | -0.3953972 | -0.3229079 | -0.2444787 | -0.1602059 | -0.0705917 | 0.0238155 | 0.1224337 | 0.2246448 | 0.3297914 | 0.4371754 | 0.5460574 | 0.6556559 | 0.7651492 | 0.8736760 | 0.9803381 | 1.0842038 | 1.1843108 | 1.2796713 | 1.3692762 | 1.4521010 | 1.5271118 | 1.5932710 | 1.6495450 | 1.6949113 | 1.7283663 | 1.7490295 | 1.7568367 | 1.7521493 | 1.7353726 | 1.7069491 | 1.6673551 | 1.6170963 | 1.5567052 | 1.4867372 | 1.4077677 | 1.3203890 | 1.2252074 | 1.1228404 | 1.0139134 | 0.8990570 | 0.7789042 | 0.6540872 | 0.5252349 | 0.3929694 | 0.2579035 | 0.1206377 | -0.0182427 | -0.1581701 | -0.2985978 | -0.4390016 | -0.5788831 | -0.7177709 | -0.8552231 | -0.9908283 | -1.1242073 | -1.2550137 | -1.3829349 | -1.5076916 | -1.6290383 |
| Cebpz | -0.7058591 | -0.7273201 | -0.7486146 | -0.7696388 | -0.7902901 | -0.8104669 | -0.8300687 | -0.8489962 | -0.8671507 | -0.8844345 | -0.9007507 | -0.9160026 | -0.9300945 | -0.9429304 | -0.9544149 | -0.9644522 | -0.9729464 | -0.9798012 | -0.9849194 | -0.9882032 | -0.9895532 | -0.9888689 | -0.9860479 | -0.9809859 | -0.9735762 | -0.9637093 | -0.9512729 | -0.9361513 | -0.9182247 | -0.8973695 | -0.8734573 | -0.8463546 | -0.8159225 | -0.7820159 | -0.7444831 | -0.7031655 | -0.6578965 | -0.6085013 | -0.5547962 | -0.4965875 | -0.4336717 | -0.3658335 | -0.2928462 | -0.2144853 | -0.1308773 | -0.0425259 | 0.0500284 | 0.1462220 | 0.2454653 | 0.3471403 | 0.4505996 | 0.5551643 | 0.6601243 | 0.7647373 | 0.8682298 | 0.9697980 | 1.0686095 | 1.1638053 | 1.2545031 | 1.3398003 | 1.4187788 | 1.4905090 | 1.5540560 | 1.6084850 | 1.6528682 | 1.6862922 | 1.7079527 | 1.7177890 | 1.7161268 | 1.7033302 | 1.6797958 | 1.6459490 | 1.6022404 | 1.5491426 | 1.4871465 | 1.4167584 | 1.3384966 | 1.2528883 | 1.1604669 | 1.0617689 | 0.9573317 | 0.8476904 | 0.7333760 | 0.6149128 | 0.4928165 | 0.3675922 | 0.2397325 | 0.1097162 | -0.0219934 | -0.1549497 | -0.2887238 | -0.4229056 | -0.5571042 | -0.6909489 | -0.8240893 | -0.9561958 | -1.0869594 | -1.2160921 | -1.3433261 | -1.4684140 |
| Dmrtc1a | -1.3734099 | -1.3591662 | -1.3438435 | -1.3273789 | -1.3097093 | -1.2907715 | -1.2705033 | -1.2488437 | -1.2257343 | -1.2011201 | -1.1749504 | -1.1471803 | -1.1177716 | -1.0866945 | -1.0539292 | -1.0194667 | -0.9833115 | -0.9454822 | -0.9060139 | -0.8649595 | -0.8223913 | -0.7784025 | -0.7331087 | -0.6866489 | -0.6391867 | -0.5909107 | -0.5420351 | -0.4927995 | -0.4434687 | -0.3943315 | -0.3456999 | -0.2979063 | -0.2513018 | -0.2062528 | -0.1631374 | -0.1223414 | -0.0842538 | -0.0492611 | -0.0177426 | 0.0099359 | 0.0334281 | 0.0524131 | 0.0666016 | 0.0757532 | 0.0799422 | 0.0795670 | 0.0750783 | 0.0669551 | 0.0556935 | 0.0417973 | 0.0257697 | 0.0081060 | -0.0107114 | -0.0302174 | -0.0499669 | -0.0695357 | -0.0885210 | -0.1065404 | -0.1232295 | -0.1382394 | -0.1512323 | -0.1618773 | -0.1698445 | -0.1747991 | -0.1763933 | -0.1742590 | -0.1680357 | -0.1576389 | -0.1431025 | -0.1244291 | -0.1015917 | -0.0745346 | -0.0431753 | -0.0074049 | 0.0329105 | 0.0779298 | 0.1278358 | 0.1828353 | 0.2431586 | 0.3090590 | 0.3808127 | 0.4587185 | 0.5430970 | 0.6342904 | 0.7326615 | 0.8385928 | 0.9524852 | 1.0747568 | 1.2058405 | 1.3461822 | 1.4962377 | 1.6564699 | 1.8273442 | 2.0093252 | 2.2028707 | 2.4084264 | 2.6264194 | 2.8572512 | 3.0000000 | 3.0000000 |
| Hbp1 | -2.2416182 | -2.1775526 | -2.1123486 | -2.0460563 | -1.9787309 | -1.9104325 | -1.8412263 | -1.7711827 | -1.7003778 | -1.6288928 | -1.5568150 | -1.4842369 | -1.4112570 | -1.3379795 | -1.2645143 | -1.1909771 | -1.1174893 | -1.0441776 | -0.9711747 | -0.8986182 | -0.8266511 | -0.7554214 | -0.6850817 | -0.6157892 | -0.5477052 | -0.4809949 | -0.4158267 | -0.3523725 | -0.2908064 | -0.2313048 | -0.1740457 | -0.1192083 | -0.0669720 | -0.0175165 | 0.0289795 | 0.0723386 | 0.1123855 | 0.1489475 | 0.1818556 | 0.2109451 | 0.2360561 | 0.2570346 | 0.2737332 | 0.2860215 | 0.2940073 | 0.2980424 | 0.2984976 | 0.2957507 | 0.2901834 | 0.2821807 | 0.2721284 | 0.2604123 | 0.2474171 | 0.2335252 | 0.2191163 | 0.2045671 | 0.1902507 | 0.1765369 | 0.1637925 | 0.1523815 | 0.1426661 | 0.1350073 | 0.1297660 | 0.1273045 | 0.1279880 | 0.1321861 | 0.1402382 | 0.1521899 | 0.1679462 | 0.1874172 | 0.2105178 | 0.2371678 | 0.2672909 | 0.3008141 | 0.3376675 | 0.3777835 | 0.4210962 | 0.4675411 | 0.5170547 | 0.5695737 | 0.6250347 | 0.6833741 | 0.7445269 | 0.8084270 | 0.8750063 | 0.9441948 | 1.0159196 | 1.0901049 | 1.1666715 | 1.2455367 | 1.3266133 | 1.4098101 | 1.4950310 | 1.5821748 | 1.6711353 | 1.7618003 | 1.8540520 | 1.9477666 | 2.0428139 | 2.1390573 |
| Sp7 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341186 | -0.4341184 | -0.4341177 | -0.4341139 | -0.4340983 | -0.4340400 | -0.4338478 | -0.4332892 | -0.4318580 | -0.4286043 | -0.4220076 | -0.4100274 | -0.3904573 | -0.3615970 | -0.3230614 | -0.2763889 | -0.2251161 | -0.1741941 | -0.1289158 | -0.0937410 | -0.0714195 | -0.0626496 | -0.0662753 | -0.0798458 | -0.1002952 | -0.1245412 | -0.1498917 | -0.1742366 | -0.1960650 | -0.2143656 | -0.2285667 | -0.2390056 | -0.2462552 | -0.2507196 | -0.2526686 | -0.2522620 | -0.2495662 | -0.2445636 | -0.2371570 | -0.2271689 | -0.2143375 | -0.1983075 | -0.1786183 | -0.1546861 | -0.1257816 | -0.0910020 | -0.0492352 | 0.0008836 | 0.0610248 | 0.1332297 | 0.2199881 | 0.3243320 | 0.4499461 | 0.6012988 | 0.7837936 | 1.0039437 | 1.2695686 | 1.5900105 | 1.9763680 | 2.4417355 | 3.0000000 | 3.0000000 | 3.0000000 | 3.0000000 |
| Onecut2 | -0.2233659 | -0.2323474 | -0.2411131 | -0.2496660 | -0.2580093 | -0.2661461 | -0.2740799 | -0.2818138 | -0.2893513 | -0.2966959 | -0.3038509 | -0.3108198 | -0.3176061 | -0.3242133 | -0.3306449 | -0.3369044 | -0.3429953 | -0.3489211 | -0.3546852 | -0.3602910 | -0.3657421 | -0.3710417 | -0.3761933 | -0.3812002 | -0.3860657 | -0.3907930 | -0.3953853 | -0.3998458 | -0.4041777 | -0.4083839 | -0.4124676 | -0.4164316 | -0.4202789 | -0.4240124 | -0.4276349 | -0.4311491 | -0.4345578 | -0.4378635 | -0.4410689 | -0.4441764 | -0.4471886 | -0.4501079 | -0.4529366 | -0.4556763 | -0.4583136 | -0.4608205 | -0.4631709 | -0.4653405 | -0.4673062 | -0.4690461 | -0.4705392 | -0.4717642 | -0.4726996 | -0.4733228 | -0.4736094 | -0.4735329 | -0.4730632 | -0.4721661 | -0.4708024 | -0.4689258 | -0.4664824 | -0.4634079 | -0.4596263 | -0.4550464 | -0.4495589 | -0.4430319 | -0.4353112 | -0.4262524 | -0.4157037 | -0.4034849 | -0.3893833 | -0.3731491 | -0.3544900 | -0.3330655 | -0.3084791 | -0.2802709 | -0.2479083 | -0.2107760 | -0.1681651 | -0.1192614 | -0.0631324 | 0.0012848 | 0.0751967 | 0.1599645 | 0.2571142 | 0.3683433 | 0.4955223 | 0.6406905 | 0.8060431 | 0.9939072 | 1.2067068 | 1.4469125 | 1.7169788 | 2.0192664 | 2.3559555 | 2.7289507 | 3.0000000 | 3.0000000 | 3.0000000 | 3.0000000 |
| Nkx6-2 | -0.4381157 | -0.4443818 | -0.4504403 | -0.4562878 | -0.4619224 | -0.4673428 | -0.4725487 | -0.4775405 | -0.4823192 | -0.4868865 | -0.4912445 | -0.4953956 | -0.4993428 | -0.5030889 | -0.5066373 | -0.5099913 | -0.5131543 | -0.5161298 | -0.5189210 | -0.5215311 | -0.5239634 | -0.5262206 | -0.5283054 | -0.5302202 | -0.5319669 | -0.5335472 | -0.5349623 | -0.5362131 | -0.5372998 | -0.5382220 | -0.5389790 | -0.5395690 | -0.5399899 | -0.5402386 | -0.5403111 | -0.5402025 | -0.5399067 | -0.5394168 | -0.5387241 | -0.5378188 | -0.5366894 | -0.5353227 | -0.5337032 | -0.5318135 | -0.5296370 | -0.5271576 | -0.5243571 | -0.5212145 | -0.5177061 | -0.5138046 | -0.5094794 | -0.5046960 | -0.4994154 | -0.4935940 | -0.4871825 | -0.4801261 | -0.4723628 | -0.4638236 | -0.4544308 | -0.4440974 | -0.4327262 | -0.4202078 | -0.4064200 | -0.3912256 | -0.3744711 | -0.3559843 | -0.3355737 | -0.3130360 | -0.2881520 | -0.2606802 | -0.2303556 | -0.1968876 | -0.1599595 | -0.1192262 | -0.0743141 | -0.0248199 | 0.0296894 | 0.0896758 | 0.1556299 | 0.2280682 | 0.3075304 | 0.3945753 | 0.4897758 | 0.5937118 | 0.7069629 | 0.8300987 | 0.9636694 | 1.1081939 | 1.2641489 | 1.4319566 | 1.6119735 | 1.8044794 | 2.0096683 | 2.2276403 | 2.4583967 | 2.7018369 | 2.9577581 | 3.0000000 | 3.0000000 | 3.0000000 |
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.4 Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=TRUE, return_matrix = TRUE)
ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_0.01, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_differential_gene_test_analysis_qval_0.01_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)2.2.2.1.5 Plotting of transcription factors differentially expressed in pseudotime
2.2.2.1.5.1 Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
2.3 Selected genes
# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Kif9", "Mbp", "Nes", "Pdgfra", "Top2a")
# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))plot_pseudotime_heatmap(monocle[genes_of_interest,],
num_clusters = 1,
cores = 1,
show_rownames = T)
2.3.1 Genes in pseudotime, single branch (Selected genes)
p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)
2.3.2 Genes in pseudotime with branches (Selected genes)
p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)
p <- p %>% remove_geom("point")
show(p)
3 Seurat tSNE plots
p <- cytokit::tsne(seurat, label=FALSE)
show(p)
p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
4 Save monocle object to directory, and write pseudotime of cells to table.
save(monocle, file=file.path(monocle_objects_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)5 Session info
sessionInfo()## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 forcats_0.4.0
## [4] stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.0
## [7] tidyr_0.8.2 tibble_2.0.1 tidyverse_1.2.1
## [10] Seurat_2.3.4 cowplot_0.9.4 R.utils_2.8.0
## [13] R.oo_1.22.0 R.methodsS3_1.7.1 readr_1.3.1
## [16] readxl_1.3.0 patchwork_0.0.1 monocle_2.10.1
## [19] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-1
## [22] Biobase_2.42.0 BiocGenerics_0.28.0 Matrix_1.2-15
## [25] ggedit_0.3.0 ggplot2_3.1.0 kableExtra_1.0.1
## [28] cytokit_0.6.0 pheatmap_1.0.12 colorRamps_2.3
##
## loaded via a namespace (and not attached):
## [1] snow_0.4-3 backports_1.1.3 Hmisc_4.2-0
## [4] plyr_1.8.4 igraph_1.2.4 lazyeval_0.2.2
## [7] densityClust_0.3 fastICA_1.2-1 digest_0.6.18
## [10] foreach_1.4.4 htmltools_0.3.6 lars_1.2
## [13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.1
## [16] cluster_2.0.7-1 mixtools_1.1.0 ROCR_1.0-7
## [19] limma_3.38.3 modelr_0.1.3 matrixStats_0.54.0
## [22] docopt_0.6.1 colorspace_1.4-0 ggrepel_0.8.0
## [25] rvest_0.3.2 haven_2.0.0 xfun_0.4
## [28] sparsesvd_0.1-4 crayon_1.3.4 jsonlite_1.6
## [31] survival_2.43-3 zoo_1.8-4 iterators_1.0.10
## [34] ape_5.2 glue_1.3.0 gtable_0.2.0
## [37] webshot_0.5.1 kernlab_0.9-27 prabclus_2.2-7
## [40] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
## [43] bibtex_0.4.2 miniUI_0.1.1.1 Rcpp_1.0.0
## [46] metap_1.1 dtw_1.20-1 xtable_1.8-3
## [49] htmlTable_1.13.1 reticulate_1.11.1 foreign_0.8-71
## [52] bit_1.1-14 proxy_0.4-22 mclust_5.4.2
## [55] SDMTools_1.1-221 Formula_1.2-3 tsne_0.1-3
## [58] htmlwidgets_1.3 httr_1.4.0 FNN_1.1.3
## [61] gplots_3.0.1.1 RColorBrewer_1.1-2 shinyAce_0.3.3
## [64] fpc_2.1-11.1 acepack_1.4.1 modeltools_0.2-22
## [67] ica_1.0-2 pkgconfig_2.0.2 flexmix_2.3-14
## [70] nnet_7.3-12 labeling_0.3 tidyselect_0.2.5
## [73] rlang_0.3.1 reshape2_1.4.3 later_0.8.0
## [76] cellranger_1.1.0 munsell_0.5.0 tools_3.5.0
## [79] cli_1.0.1 generics_0.0.2 broom_0.5.1
## [82] ggridges_0.5.1 evaluate_0.13 shinyBS_0.61
## [85] yaml_2.2.0 npsurv_0.4-0 knitr_1.21
## [88] bit64_0.9-7 fitdistrplus_1.0-14 robustbase_0.93-3
## [91] caTools_1.17.1.1 randomForest_4.6-14 RANN_2.6.1
## [94] pbapply_1.4-0 nlme_3.1-137 mime_0.6
## [97] slam_0.1-44 xml2_1.2.0 hdf5r_1.0.0
## [100] compiler_3.5.0 rstudioapi_0.9.0 png_0.1-7
## [103] lsei_1.2-0 stringi_1.3.1 highr_0.7
## [106] lattice_0.20-35 trimcluster_0.1-2.1 HSMMSingleCell_1.2.0
## [109] pillar_1.3.1 combinat_0.0-8 Rdpack_0.10-1
## [112] lmtest_0.9-36 data.table_1.12.0 bitops_1.0-6
## [115] gbRd_0.4-11 httpuv_1.5.1 R6_2.4.0
## [118] latticeExtra_0.6-28 promises_1.0.1 KernSmooth_2.23-15
## [121] gridExtra_2.3 codetools_0.2-15 MASS_7.3-51.1
## [124] gtools_3.8.1 assertthat_0.2.0 withr_2.1.2
## [127] qlcMatrix_0.9.7 diptest_0.75-7 doSNOW_1.0.16
## [130] hms_0.4.2 grid_3.5.0 rpart_4.1-13
## [133] class_7.3-14 rmarkdown_1.11 segmented_0.5-3.0
## [136] Rtsne_0.15 lubridate_1.7.4 shiny_1.2.0
## [139] base64enc_0.1-3